OBI consortium

Quick Term Template: Class addition by design patternsFull tutorial available at:

http://obi-ontology.org/page/Quick_Term_Templates

OBI consortium

Philippe Rocca-Serraproccaserra@gmail.comhttp://www.isa-tools.org

Carlo Torniaitorniai@ohsu.edu

Background

• Problem: How to enable knowledge experts to add large number of classes with as little hassle as possible?– Batch processing capability– Automatic class axiomization– Identification of recurring patterns in knowledge

representation

Tools & Prerequisites

• Protégé 3.4.4• Mapping Master Plugin (O’Connor et al, 2010)

[http://protege.cim3.net/cgi-bin/wiki.pl?MappingMaster]

• An OWL Ontology• Knowledge of OWL Manchester Syntax• A use case, a pattern/formal representation!

QTT approach overview

Processing the Spreadsheet with Mapping Master

Principle: 1. Finding a pattern

• Measuring concentration of glucose in urine• Measuring concentration of calcium in plasma• Measuring concentration of CO2 in air• Measuring concentration of PSA in plasma• …….

Principle: 2.modeling step

• Measuring concentration of glucose in urine• Measuring concentration of calcium in plasma• Measuring concentration of CO2 in air• Measuring concentration of PSA in plasma

• <data> <quality> <evaluant> <analyte>

QTT example

Target Ontology: OBI.owlConstraints: • Map terms (or submit if not available) to compatible ontologies

(i.e. sharing the same top level ontology, here BFO 1.1)• Import those terms External.owl + ExternalDerived.owl files

Principle: 3. Class Definition and formalization

Principle: 4.Process with Mapping Master

Device example

Class: @A*(rdfs:label)SubClassOf: @B*(rdfs:label),has_function some @C*(rdfs:label),has_function some @D*(rdfs:label),

Future Work

• Automatic Import via MIREOT mechanism of external and externalDerived.owl files (or equivalent structure) in target ontology during QTT processing

• Creation of a library of QTT available from OBI– Analyte template– Service template– Instrument template– Single nucleotide mapping structure assayMore if people willing to share!

Reference / Acknowledgements

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

P. Rocca-Serra, A. Ruttenberg, M. J. O'Connor, T. Whetzel, D. Schober, J. Greenbaum, M. Courtot, S. A. Sansone, R. Scheurmann, B. Peters ( & OBI consortium)

Journal of Applied Ontology, 6, 13-22. Published in 2011TUTORIAL:http://obi-ontology.org/w/images/d/dd/Howto-QTT-

Template-Import-MappingMaster.doc